6S0V

The crystal structure of kanamycin B dioxygenase (KanJ) from Streptomyces kanamyceticus in complex with nickel, neamine and sulfate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

A study on the structure, mechanism, and biochemistry of kanamycin B dioxygenase (KanJ)-an enzyme with a broad range of substrates.

Mrugala, B.Milaczewska, A.Porebski, P.J.Niedzialkowska, E.Guzik, M.Minor, W.Borowski, T.

(2021) FEBS J 288: 1366-1386

  • DOI: 10.1111/febs.15462
  • Primary Citation of Related Structures:  
    6S0R, 6S0T, 6S0S, 6S0V, 6S0U, 6S0W

  • PubMed Abstract: 
  • Kanamycin A is an aminoglycoside antibiotic isolated from Streptomyces kanamyceticus and used against a wide spectrum of bacteria, including Mycobacterium tuberculosis. Biosynthesis of kanamycin involves an oxidative deamination step catalyzed by kanamycin B dioxygenase (KanJ), thereby the C2' position of kanamycin B is transformed into a keto group upon release of ammonia ...

    Kanamycin A is an aminoglycoside antibiotic isolated from Streptomyces kanamyceticus and used against a wide spectrum of bacteria, including Mycobacterium tuberculosis. Biosynthesis of kanamycin involves an oxidative deamination step catalyzed by kanamycin B dioxygenase (KanJ), thereby the C2' position of kanamycin B is transformed into a keto group upon release of ammonia. Here, we present for the first time, structural models of KanJ with several ligands, which along with the results of ITC binding assays and HPLC activity tests explain substrate specificity of the enzyme. The large size of the binding pocket suggests that KanJ can accept a broad range of substrates, which was confirmed by activity tests. Specificity of the enzyme with respect to its substrate is determined by the hydrogen bond interactions between the methylamino group of the antibiotic and highly conserved Asp134 and Cys150 as well as between hydroxyl groups of the substrate and Asn120 and Gln80. Upon antibiotic binding, the C terminus loop is significantly rearranged and Gln80 and Asn120, which are directly involved in substrate recognition, change their conformations. Based on reaction energy profiles obtained by density functional theory (DFT) simulations, we propose a mechanism of ketone formation involving the reactive Fe IV  = O and proceeding either via OH rebound, which yields a hemiaminal intermediate or by abstraction of two hydrogen atoms, which leads to an imine species. At acidic pH, the latter involves a lower barrier than the OH rebound, whereas at basic pH, the barrier leading to an imine vanishes completely. DATABASES: Structural data are available in PDB database under the accession numbers: 6S0R, 6S0T, 6S0U, 6S0W, 6S0V, 6S0S. Diffraction images are available at the Integrated Resource for Reproducibility in Macromolecular Crystallography at http://proteindiffraction.org under DOIs: 10.18430/m36s0t, 10.18430/m36s0u, 10.18430/m36s0r, 10.18430/m36s0s, 10.18430/m36s0v, 10.18430/m36s0w. A data set collection of computational results is available in the Mendeley Data database under DOI: 10.17632/sbyzssjmp3.1 and in the ioChem-BD database under DOI: 10.19061/iochem-bd-4-18.


    Organizational Affiliation

    Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Kanamycin B dioxygenaseA, B, C, D, E, F288Streptomyces kanamyceticusMutation(s): 0 
Gene Names: kanJkacB
EC: 1.14.11.37
Find proteins for Q6L732 (Streptomyces kanamyceticus)
Explore Q6L732 
Go to UniProtKB:  Q6L732
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XXX
Query on XXX

Download Ideal Coordinates CCD File 
DA [auth E], JA [auth F], K [auth A], O [auth B], S [auth C], Y [auth D](1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside
C12 H26 N4 O6
SYJXFKPQNSDJLI-HKEUSBCWSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth E] , BA [auth E] , CA [auth E] , FA [auth F] , GA [auth F] , H [auth A] , HA [auth F] , I [auth A] , 
AA [auth E],  BA [auth E],  CA [auth E],  FA [auth F],  GA [auth F],  H [auth A],  HA [auth F],  I [auth A],  IA [auth F],  J [auth A],  M [auth B],  N [auth B],  Q [auth C],  R [auth C],  U [auth D],  V [auth D],  W [auth D],  X [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
EA [auth F], G [auth A], L [auth B], P [auth C], T [auth D], Z [auth E]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.467α = 90
b = 185.25β = 94.68
c = 110.46γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Polish National Science CentrePoland2014/15/B/NZ1/03331
National Institutes of Health/National Human Genome Research InstituteUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Derived calculations, Structure summary
  • Version 2.1: 2020-11-25
    Changes: Database references, Structure summary
  • Version 2.2: 2021-02-24
    Changes: Database references